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The Boston School Committee approved a historic agreement last night to establish greater cooperation between the city and independent charter schools, in an effort to provide more students across the city with a stronger education.

A key component of the agreement calls for the city’s school system and the more than dozen charter schools - autonomous public schools overseen by the state - to share innovative educational practices that are getting results in boosting student achievement.

The measure passed on a 5-to-2 vote.

But the agreement also has sparked controversy, in particular a clause that encourages the city to lease vacant school buildings to charter schools, a move that could allow charter schools to more easily expand in a city with a tight real estate market.

Mayor Thomas M. Menino, who brought the two sides together in a meeting earlier this spring to hash out the agreement, is planning to sign it today at a ceremony in Roxbury.

“I’m looking forward to working with the superintendent and the charter schools to make sure the compact is implemented to the letter of the law,’’ Menino said before the meeting.

The signing ceremony is part of an orchestrated campaign by the Bill & Melinda Gates Foundation, which has been pushing cities nationwide to form such agreements.

Boston is among three cities signing compacts today. The other two are Central Falls, R.I., and Sacramento, Calif.

They will join nine other cities - from Los Angeles to New York City - that have put charter compacts in place.

The move in Boston could enable the city to receive a $100,000 grant from the foundation to help execute the compact.

In many ways, the compact represents a truce between the city and the charter schools after years of acrimony that dates back to when the charter schools first began opening in the mid-1990s.

Much of the fighting has been over the way the state funds them. Boston pays out about $55 million a year from its state education aid to cover the charter school tuition costs of about 5,000 city children.

City leaders have long argued that charter schools have courted the best and brightest students to enroll in their schools and have encouraged students who do not measure up - either academically or discipline-wise - to go back to the city’s school system.

Charter schools have repeatedly denied those assertions, saying they seek to educate students of all abilities and admit students through a blind lottery.

While charter schools educate a higher percentage of African-American students than the city’s school system, they tend to enroll fewer students with special needs or limited fluency in English.

As part of the compact, the charter schools will more aggressively recruit students to better reflect the city’s demographics.

The Boston Teachers Union opposes the compact because the charter schools could lease city school buildings and because charter schools could send students with autism and other severe special needs to the school system’s specialized programs.

“Charter schools want to say they embrace special education students but sign a compact that allows them to push them back to the city’s school system,’’ Richard Stutman, the union’s president, said before the meeting. “It’s a one-way compact. The city gets very little and gives a lot.’’

The School Committee was also scheduled last night to vote on a set of rules for public participation at its meeting, which was held at School Department headquarters on Court Street.